Chaos
by Synobis
Summary: Takes place after Sonic Heroes. Shadow and Rouge try to steal an emerald from Eggman, but it turns for the worst. RougexShadow in later chapters. R
1. Default Chapter

Disclaimer: I don't own any of the Sonic characters, none, zip, nada. If I do, I certainly didn't know about it and am wondering were all my money is and why the hell I'm not living in a bigger house. Anyway, now that we have established that I don't own anything, except for any OC I decide to put into the story, lets move on.

Notes: This is actually my first posted fic, I hope everyone who reads it is able to enjoy it as much as I did writing it. Plz feel free to put forth any suggestions and I will see if they are able to fit into what I have planned for the story.

It was the early hours of the morning, and Shadow lay awake pondering over events just passed. He had joined with Rouge and Omega, aided in the destruction of Eggmans air fleet, and played a part in the defeat of Metal Sonic. But what he had failed to learn was why he was in the capsule, and whether or no he was original or just a copy. A fake. The word stung him as nothing ever could. The though of him being a mere image caused anger to swell up inside him. He had managed to learn who he was, or at least who he was supposed to be, from Rouge. She had told him how he was created and why, even showing official government records to back up her statements. She had also told him what she knew of the insident back on ARK, and although all this information seemed familiar and he recognized several parts of it, the question still lingered: was he the original? The noise of other life broke him from his deep thoughts. Rouge had awakened. She was probably in the bathroom readying herself as usual. After their last encounter with Eggman, Rouge had surprised him with her offer to let him stay at her place, and since he had no where else to go, he accepted. In the time they had been spending together the pair had gotten a lot closer, Shadow even began to feel something for her he hadn't felt in a long time. But it was something he felt he couldn't admit, not yet anyway. 

"Hmm, look who's awake." Rouges voice rang, "What brings you out of the coffin so early?" 

Shadow had been sleeping in a lot lately, so he wasn't surprised at the question. He sighed before making his reply, "I don't know…" 

Rouge frowned at the cryptic answer and went into the kitchen. "Really…" 

She sounded kind of disappointed. Rouge had been trying to get him to open up more, but it was kind of hard for him. 

"You know, I got a call from Sonic," 

Shadow growled at the mention of his blue counter-parts name. He didn't know why, but he didn't really like Sonic all that much. Maybe it was his Arrogance or his attitude, but he didn't really care at the moment. Rouge had obviously heard him because of her change in tone, 

"You know, all he wants to do is talk. He says Tails found out some things about why you where in the capsule, and you haven't really bothered to question them much." 

This was true, Shadow hadn't bothered on questioning Sonic, it wasn't something that was on his mind. Shadow remained silent on the matter until Rouge walked in and sat in front of him. 

"Look, I know you don't like Sonic all that much, he's not my favorite person either, but isn't it worth the information at least?" Rouge's expression and tone made it hard for him to deny her. 

"Fine…but if he pisses me off…" 

Rouge nodded and stood up, "Well, that's fine I guess, let me finish up some things and then we can leave."

Shadow skidded to a halt in front of Tails workshop, a cloud of dust rushing past him from the sudden stop. As the cloud settled he set Rouge down. They had been walking to the train station, but since Shadow had wanted to get the whole ordeal done and over with as soon as possible, he had scooped up Rouge and ran to their destination. Rouge had obviously been very surprised at his suddenness, and he couldn't help but chuckle as she turned around and tried to hit him. 

"You jerk! You scared the hell out of me! Couldn't you have at least warned me?" Shadow ducked the first one and caught the second hit, turning her around and pulling her back against his chest, and effectively restraining her from trying to hit him again, but made sure not to hurt her. 

"Ok, ok, I'm sorry. Ill warn you next time." Shadow chuckled, "As long as you stop assaulting me, I want to get this over with as soon as possible." 

Rouge was speechless for a moment; it wasn't often that Shadow had made physical contact unless he was fighting. Usually he just dodged. And his voice…it actually sounded like he had some fun with that, it was usually so monotone. She couldn't help but blush at the unexpected turn of events. 

"Fine." She stammered, trying not to give away how she felt. 

She might have said more, but it was then that Sonic and Tails decided to make themselves known. 

"Aww, how cute! Didn't know you had it in you Shadow!" Sonic laughed as Tails merely grinned at the scene. 

Rouge instinctively pulled away from Shadow as he let her go, blushing, as she knew what it probably looked like. Shadow on the other hand looked like he wanted to kill Sonic then and there. Rouge decided to say something before it become more than just a look.

"Yeah, yeah. Look blue boy, just cause you can't have me doesn't mean you need to poke fun." Shadow lifted an eyebrow at this and Sonic merely chuckled. 

"Well?" Rouge inquired, "You invited us here and aren't going to let us in?" 

Sonic motioned for them to come inside and led them to Tails' computer. Once everyone was seated Tails began to tell what he had found. 

"According to what I found in Eggmans database, he found Shadow in a weakened state in an unnamed location after he fell through the atmosphere. The capsule he had Shadow in was meant to not only keep him in stasis, but accelerate his recovery, allow Eggman to manipulate Shadow's memories, and let him implant whatever he wished into Shadow's body." Tails brought up some schematic on his computer illustrating the capsule and its functions before continuing. 

"Eggmans original plan had been to infuse you with the Chaos' powers and replace your memory with only what he wanted you to remember, but before he could finish Metal found out about it and decided he wanted the power for himself so he could destroy both you and Sonic." 

Rouge was slightly alarmed by this, "What do you mean 'before he could finish?'" 

Tails brought up some charts on his computer, "See here? The process was started, but wasn't finished. So Shadow does have some of Chaos' powers in him. Just not like what Metal had. It will probably just increase Shadow's Chaos abilities." 

Shadow thought of what he had recently gained abilities to do. His Chaos powers had increased dramatically, but they only did so when he was actually near a Chaos Emerald. But the things that he normally needed a Chaos Emerald for, like Chaos Control and Chaos Spear, he was now able to perform on a whim. He had also mastered some new attack techniques since he had moved in with Rouge, one of them he liked especially, he called it Chaos Nightmare. It created a small shockwave of Chaos energy around his hands, throwing whatever was near him back violently. He decided he had gained all he wanted to know from Sonic and Tails and got up to leave. 

"Shadow? Where are you going?" Rouges voice inquired. 

Shadow turned and looked at her. "Going to take a run, I want to think about some things. Ill see you back at your place." 

And with that he was gone. 

Shadow ran a long way before taking rest on cliff overlooking a green valley. He sat down on a rock nearby and began to gather his thoughts. 

"Well, at least I'm original." He mused.

The thought was satisfying to him; it made him more at ease with himself. But the fact the Eggman had wanted to wipe his memories angered him. Shadow also wanted to confront Eggman and find out more detailed information about this Chaos creature and just how far the extent of the effects of him being infused with it went. Questions only Eggman himself could answer. Shadow looked up and found that it was growing dark around him, he had been out longer than he thought. Shadow decide he had stayed out long enough and started toward the city, taking to the rooftops once he was near enough. He didn't like to show himself to the general public. Even though he had been pardoned for his actions after his release by Eggman due to his aid in stopping ARK from crashing into the Earth and helping stop Eggmans air fleet, the general public still felt uneasy with his presence. The few times he had gone out into public he could feel the people's fear of him. Everyone got out of the way when he walked in a crowd and placed their eye's upon him, something he didn't like in the least. 

"Being a living weapon and trying to destroy the planet tends to get you that kind of reputation." Shadow thought as he went from rooftop to rooftop. 

When he finally got to Rouge's apartment he found her on the couch watching something on the news. 

"Feel better?" She asked. 

Shadow joined her on the couch. "Yeah…though I would like to get a hold of Eggman. I want to know just what the extent of what he did is. But I'm not sure where to start looking." 

Rouge smiled at this, "You know, being a government spy does have its advantages." Shadow glanced over at Rouge, his interest perked. "I have reports of his activities in a concealed canyon base not far from here. He isn't doing too well of a job in concealing it, seems he was purposely building it so others could find it." 

Shadow thought for a moment. "Why didn't you mention this to Sonic and Tails back at their place?" 

Rouge gestured towards the TV. "Take a look." 

The news was showing pictures of the Federal Reserve Bank, where the one of the Chaos Emeralds had been placed. The 1-ton vault door had been completely removed from its hinges and thrown across the room. 

"As you know, the Chaos Emerald was being kept at the bank. And who do we know who can make something capable of ripping a 1-ton door of its hinges and throwing it like it was nothing?" Rouge asked. 

Shadow didn't even need to respond, they both already knew. After a moment of silence Shadow looked over to Rouge. 

"You didn't tell the others because you want to steal the emerald, don't you?" 

Rouge gave him a sly grin, "You certainly know a woman's heart don't you? Think of it this way, you'll get to confront Eggman _and_ we get a Chaos Emerald." 

Shadow didn't really need further encouragement. "Very well, we head out tomorrow then?" 

Rouge nodded and headed to her room, "Night Shad." 

Shadow was left to himself for the moment. He really didn't like being called that, but o well. After a moment of thought he too retired into his room. 

Their adventure was about to begin.

End notes: I will try to post the next chapter soon, plz review. =)


	2. New Weapons

Notes: I appreciate all those who enjoyed my previous chapter enough to review. I hope that this chapter entertains you all as well as the previous one.

The morning found Rouge and Shadow making their way through the Mystic Ruins, they had gotten up early and decided to take a less direct approach into Eggman's base. Rouge had found an area of the base that was the most vulnerable area from which to enter; this would hopefully ensure a quick end to their assault. The part of the jungle they were making their way through was rather thick. The several trees and dense undergrowth served to conceal their movements. Soon the jungle gave way to a cliff, one with an excellent view of Eggman's base. It was medium sized, barely concealed within the cliff walls. It was just enough so that an average person would not have been able to easily spot it, but enough so one as seasoned as Rouge was in such matters could easily take into account some of the more subtle signs. Rouge looked down on the base, taking out a pair of high-resolution digital binoculars and began scanning the base to get a secure figure of the amount of defenses they would have to make their way through before reaching Eggman himself. The defenses seemed crude and lacking, even by Eggman's standards. It wouldn't be a problem to get passed them. She lowered the binoculars and looked over at Shadow, smiling.

"Seems Eggman hasn't had enough time to put up all his defenses, shouldn't be a problem for the worlds greatest treasure hunter and the ultimate life-form."

Shadow merely nodded, a serious expression on his face. He had also taken a look at Eggman's base, only he didn't need binoculars. Rouge pointed to an area of the base that not far from their current position.

"That area will be the best place to enter, from there we can proceed inside the main building and get that emerald!"

Rouge spread her wings and motioned to Shadow, who in turn sighed. He generally didn't like to be carried by anyone, he felt it restricted a measure of control he had, but he reluctantly jumped up and took Rouge's hand. As the pair flew over the base to get to their destination Eggman's defenses kicked in and turrets began to come to life, with them as prime targets. Rouge managed to avoid all their fire, though it was more difficult for her to maneuver with Shadow's added weight, even if she had grown more used to it. Shadow wasn't standing idle though, and was entertaining himself by using his Chaos Spear on any unfortunate turret within his sight. Even though Shadow detested Eggman, one had to marvel at his ability to create such things in so short a time span. Shadow and Rouge touched down just outside the central building within the base; a wake of twisted metal left behind them. The base was on full alert now; blaring alarms notified the rest of the compound that unwelcome guests had arrived. Shadow wasted no time once he had dropped from Rouge's hold, Eggman's robots had quickly made an appearance, but Shadow was dispatching them effortlessly and keeping them off Rouge, who had been quick as well. Once Shadow was free she had made her way to a security console next to a large blast door, leading to the inside of the building, and but her spy skills to work hacking into Eggman's security systems to open the door. In no time Shadow stood in the midst of the hulking remains of Eggman's ineffective forces as Rouge concluded her work on the door, causing it to emit a hiss of protest at it worked open. 

The inside of the structure was vastly different from the outside of the base, which was adorned with Eggman's traditional colors and decals portraying his face. The walls and floors were all a dull gray, seeming as if he hadn't had time to finish his decorating. But this wasn't the first thing that the pair noticed as they entered the building; it was what seemed to be a complete lack of defenses. Rouge knew, from her previous work with Eggman, that he deployed his defenses long before he ever completed his compounds. Shadow cautiously took the lead as Rouge followed closely behind. The gray halls seemed to stretch indefinitely in what looked to be a downward spiral. Neither Shadow nor Rouge spoke on their decent, both being on alert for any possible surprise attacks that might be intended to catch them with their guard down, but the only sounds heard was deafening silence and the occasional hum of machinery from unseen sources. Their decent came to a sudden halt at a medium sized blast door, but no doubt fairly thick. The door had Eggman's traditional red frame and the trademark symbol of his face stamped across the door's center. Rouge walked over to a panel near the door and got to work. 

"This must be the end of the line, Eggman and his emerald must be on the other side of this door."

Shadow nodded, "We should proceed with caution, it's not usual for Eggman to leave any part of his base unprotected. What ever he has behind this door must be big."

Rouge agreed. Eggman must have been very confident about what lay in wait behind the door. Rouge moved from the panel, her work finished, as the doors slide open and revealed what lay beyond. The room behind the door was in a circular shape with a domed ceiling, in the center of the room was Eggman's trademark symbol, and the yellow Chaos Emerald, which resting inside a large metal pillar stretching from the floor and into the ceiling. Eggman was no where in sight. It didn't take a genius to conclude that this was a trap. The pair entered the room, and as expected, the blast door slammed shut behind them. It was obvious that although the good doctor was not physically present in the room, he had been watching them. Shadow looked over to Rouge, she was tense, her body anxious with the suspense of the unknown enemy they were most likely about to face. He, on the other hand, was keeping his cool demeanor, betraying no emotion as to what he may be feeling. 

Eggman's voice echoed across the room from an unseen source.

"Welcome! Shadow, Rouge! You aren't quite the visitors I had hoped for, but no matter, you shall be the first to taste the power of my greatest of creations! Not even you Shadow, the so-called 'Ultimate Life-Form,' stands a chance!"

Shadow smirked defiantly, "You really think your cheap toys can defeat me? Once I've crushed your paltry creation, you will have the pleasure of answering a few of my questions."

Eggman's trademark laugh filled the room.

"I know why you're here Shadow, wondering why you were in that capsule aren't you? Why don't you and Rouge join me? It wouldn't be wise to alienate you future emperor."

Rouge laughed at this comment, "I don't think so, I'm still waiting for that payment you owe me from ARK."

Eggman was obviously angered by this, "You double-crossed me bat girl! No matter.if you wont join me then I'll destroy you along with everyone else who gets in my way!"

An audible click sounded as Eggman turned off the unseen intercom, moments later an electric hum was heard. The pillar in the center of the room began to be pulled into the ceiling while the part of the floor adorned with Eggman's symbol began to open up. Rouge gasped, as she knew this would be her last chance if she wanted the emerald. Rouge spread her wings and quickly flew towards the ascending pillar to snatch the emerald.

"Rouge!"

Shadow's protests filled her ears, but she ignored them, she wanted that emerald. Rouge reached the emerald and reached towards it, but when she touched it a searing pain ripped through her body as the harnesses power from the emerald reacted from her touch.

"ROUGE!"

Shadow yelled as he saw her body jerk from the emerald power. The shock dissipated, releasing her from its grasp and gave her limp form to gravity's power. Shadow dashed towards her, catching her before she made contact with the metal floor below.

Rouge's vision was blurred, she had momentarily passed out from the sudden shock, but as her vision returned she saw Shadow over her, a worried look on his face. His ruby eyes were filled with concern, his lips moving, but no sound. As her senses fully recovered she made out his voice.

"Rouge! Say something!"

It was then that she realized she was lying in Shadow's arms. 

"Ugh.I'm.I'm ok."

Rouge managed a weak smile as she got back on her legs. The shock hadn't really been to bad; she just hadn't been prepared for it. She looked over at Shadow, who had turned over his attention to the now raised platform once he had been assured that she was ok, and couldn't help but smile at his concern for her. Rouge then looked over at the platform. It had five capsules on it, each one similar to the ones that the Shadow clones were found in on Eggman's airship during the whole Metal Sonic incident. Eggman's voice came over an unknown intercom as the capsules began to activate a hiss escape each one and surrounding it in a fine white mist.

"Witness you executioners! What a fitting end for the two of you to be killed by both your friends _and_ yourselves! _Hahahahaha_!" Both Shadow and Rouge looked on as the white mist cleared, and both were shocked at what it revealed. The mist had fallen away, allowing them to come face to face - with themselves. Beside their duplicates were identical copies of Sonic, Knuckles, and Tails.

"Wh-what is this?"

Rouge's voice was visibly shaken at the picture before her. Eggman's booming voice came from the speakers, now seeming to be everywhere at once.

"They, my dear friends, are you cybernetically enhanced clones! Not only do they match you all in your abilities, speed, strength, and thought patterns, but they exceed them as well! Through my implants they have a special muscle enhancing net surrounding their muscular system, effectively making them stronger than you are! Not only that, but the other implants within them allow them to communicate non-verbally and give their complete allegiance to me!"

Once more Eggman's insane laughter filled the room; it was enough to make one sick. A click was heard signifying the end of Eggman's gloating. This also seemed to signal the genetic copies, as they began to advance forward with looks of shear hatred on their faces. Shadow summed up his foes, the five of them against just him and Rouge. Shadow knew he probably could have taken them if it had not been for the clone of himself and Sonic. Knowing their only chance would be to escape and tell the others what was happening, then come back with a full force to neutralize this threat. He was about to make his move when he heard the icy, hate filled voice of his copy speak up.

"I know what you're thinking, that pillar you saw earlier uses the Chaos Emerald to encase this room in a Chaos resistance energy shield. Chaos Control is useless."

With the end of those words his clone attacked him, Shadow blocked the blow, but was met by another assault at his side. Shadow managed to ready himself and avoid the blows full effects, just as Knuckles came in with a furry of punches. Shadow found himself on a constant defensive as the combined assault wore at him. Though considering the odds, he was doing admirably, but it wouldn't be long before he wouldn't be able to continue at the current pace. Shadow knew he had to do something, and do it fast if both he and Rouge wanted to get out alive. Knuckles and Sonic came in for another attack, but he managed to block Knuckles punch, using the momentum to flip over him, and thus avoiding Sonic's spindash. But in doing that he had left himself open to an attack by his copy who delivered a powerful blow to his back and sent him flying towards Knuckles, who quickly uppercut him. The blow caused Shadow to be sent spiraling upwards, where he saw Sonic closing in with a spindash. Shadow barely managed to put up what defense he could before Sonic made contact. He had managed to block the force of the blow, but not Sonic's quills, which dug into his flesh. Shadow winced as he felt his arms being violently ripped open; blood spilling forth from the fresh wounds. Shadow dropped to the ground, grabbing one of his arms and soaking his white glove crimson. Taking a chance, Shadow looked over to see how Rouge was faring. She had been having her own troubles. While the clones of Shadow, Sonic, and Knuckles had been busy engaging the real Shadow, Rouge had been fighting her own copy and one of Tails. Not only was her synthetic meeting her blow for blow, but the clone of Tails proved to be much more vicious than Rouge had ever thought the fox could be. At the beginning of the fight Rouge had been on the offensive, trying to quickly defeat her assailants so she could aid Shadow, who was being worn down by all the injuries he was taking. Rouge was now on the defensive, she knew she might be trapped, but she wouldn't go down easily!

Shadow hit the wall behind him hard, making a loud thud as his body impacted with the wall and left a bloody imprint. The combined assaults from his assailants had caused him to sustain a lot of damage, the quills from his double and Sonic doing a lot of damage since they always seemed to target him when he had his hands occupied. Shadow began to feel dizzy, but quickly recovered and took a quick look around the room hoping to spot some chance of escape. The room was completely secured.with the exception of the pillar that contained the yellow Chaos Emerald. Rouge had apparently stopped its ascent, as a small portion of it was still sticking out form the ceiling. This was their one and only chance. Shadow propelled himself from the wall and ran towards Rouge, grabbing her and flinging her over his shoulder.

"Rouge, I have an idea, hang on!"

Gathering what energy he had left, Shadow sent a powerful Chaos Spear into the pillar, making a hole where the pillar went up to the surface. Shadow blasted full speed up the domed walls and into the cylindrical tube where the pillar used to be, grabbing the yellow emerald as it fell towards the floor, and ran towards the surface with the copies in hot pursuit. Upon reaching the surface, Shadow yelled out the words that would deliver them to safety. 

"_Chaos Control!_"

A blinding flash enveloped Shadow and Rouge, warping the pair away from Eggman's base and to a safer location, and leaving the clones without targets.

Tails was outside his workshop working on some new additions to his beloved place, the Tornado II, when a bright flash of light stopped him from his work. On regaining his vision he saw Rouge over an unconscious and bloodied Shadow.

"Shadow? Shadow!"

Rouge's voice was panicked. Shadow was bleeding pretty badly, cuts and bruises all over his body from the forceful assault he had just endured. Rouge looked around and noticed Tails.

"Just don't stand there! Do something!"

This broke Tails from his shock at seeing the bat and bloodied hedgehog just appear from no where. Tails proceeded to help Rouge take Shadow to a bed in his workshop until he could get some adequate supplies to properly tend to the black hedgehog.

"Hang on a sec, I'll go get Sonic and some medical supplies."

Tails ran out of the room leaving worried Rouge behind. Shadow was not in good shape, the white bed sheet were already turning crimson from his rapid loss of blood. Rouge was felt that he might die, such severe injuries were fatal to normal people. Rouge new that Shadow had a much better healing ability than the normal person, but her logical mind and her feelings were not coordinating at the moment. Tails returned a second later with Sonic behind him carrying medical supplies. Sonic set down the medical supplies near Shadow's resting place on the bed as Tails began to clean the wounds.

"Rouge, go with Sonic and tell him what happened, I'm going to need some privacy to work."

Rouge wanted to protest, but before she could Sonic placed his hand on her shoulder. Rouge knew there wasn't much she could do to help, so she reluctantly followed Sonic into the living room area of Tails' workshop. Sonic and Rouge sat across from each other, neither one really saying much for a few moments. Sonic knew Rouge probably felt something for Shadow, so he didn't know what to say to help her bear his condition better. After a moment Rouge broke the uncomfortable silence and began to tell Sonic of the events that had transpired.

"Eggman has a base in the northern part of the Mystic Ruins, where it meets with the Canyons. Me and Shadow went to there to get a Chaos Emerald he stole a few days ago and to question him about what he was doing and why Shadow was in that capsule I found him in. But when we got to the emerald he used this new force.these clones of us. He said they all not only had all our abilities and memories, but surpassed us in ever way. Eggman also said he had some kind of device on them that allowed them to communicate telepathically or something, as well as making them completely loyal to him."

Sonic was clearly agitated by this.

"Clones? Of all of us? You mean robot clones right?"

Sonic learned about the biological clones that Eggman had made of Shadow, but he knew that robotic ones had existed as well. But Rouge shook her head at his latest question.

"No.real organic ones. They have all our strengths and weaknesses, and know all our moves and abilities."

Neither Sonic nor Rouge spoke for the rest of the day, and it wasn't until nightfall that Tails emerged from the room in which he was treating Shadow. When Tails came out to them he gave them the news on Shadow's condition.

"Shadow will be fine. I cleaned his wounds and stanched the bleeding, but he was already began to show signs of recovery. If all goes well he might even be back to normal in a couple of days."

Rouge felt a wave of relief wash over her. Tails, who had been holding the Chaos Emerald Shadow had taken with him, left Rouge and Sonic to go wash up and place the emerald in a more secure area. On his return Tails got Sonic to follow and notify him on why Shadow was in his condition, as the two left Sonic told Rouge one last thing.

"Rouge, I'm going off to help Tails with some stuff, if you want to sleep we have a spare bed in the basement."

Rouge nodded and waited for the pair to leave before moving. Once they were gone she got up and went into the room Shadow was being kept in. He looked a lot better than he had when they arrived. The bed sheet had been exchanged for a clean one, the original one soaked crimson, was placed in another part of the room with the rest of the bloodied objects Tails had used to help Shadow. Rouge was rather impressed really, the fox knew a lot more about medical practices than she thought. Shadows wounds had all been bandaged in a professional manner, protecting them from any foreign objects that could cause the wounds infection. Rouge sat in the chair next to the bed Shadow was laid on and thought for a moment. To think that he would be ok.and so soon. Rouge's thought soon began to overwhelm her, causing her to fall into a deep slumber still in the chair. The following day would bring a host of new challenges for all of them to face.

End Notes: I enjoyed writing this chapter, it worked out better than I had hoped. Once more I will try to post the next chapter as soon as I am done with it, and plz remember to review! =)


	3. Chapter 3

Disclaimer: I don't own the Sonic franchise. Sega does.

Authors Note:

I realize I have not updated this in a very long time, but I found some chapters I had written for this sotry and never got around to transfering from paper to computer. I will see if I can finish this story, but I will not garuntee anything. Hope all of you who wanted me to post another chapter enjoy this one.

**Chaos**

_Chapter 3_

Shadow woke to a dark silence, his head pounding from unknown causes. Slowly, he got up and tried to assess his current location. He was in someone's room apparently, and from the looks of it he could guess where he was. Suddenly all his memories came rushing back to him, the clones, the emerald….and Rouge. On remembering Rouge, Shadow quickly jumped from the bed and rushed from the room. His sudden exit startling Sonic, who was sitting on the couch facing both the doorway Shadow emerged from and the TV he had been watching.

"Shadow? I didn't think you would be good for another few days…"

Shadow eyed Sonic for a moment before making his smirked response.

"Hmph…I've seen worse. Where is Rouge? She ok?"

Sonic pointed to a door down the hall.

"Your girlfriend is in the basement, down the hall and to the left. She fell asleep on your bed you know, real worried about you. We placed her in the basement bedroom when we got back yesterday."

Sonic's answer had also been meant to irritate Shadow, but he paid little heed to it and moved towards the door Sonic had indicated. The basement-converted-bedroom still retained many aspects of what it was prior; the only real changes being that there were no water pipes or anything similar in plain sight. The room only contained a cabinet/dresser, a few boxes, and the bed Rouge was currently sleeping on. The basement was also divided into two parts, a wall blocked off access to the rest of the basement, the only visible access point being a large, sophisticated looking metal door with a card slot next to it. Shadow sat on a box near Rouge's bed and started thinking. He found himself not only worried about Rouge, but what he, no, all of them, were going to do about the new threat Eggman had unleashed.

Rouge stirred slightly, snapping Shadow from his thoughts, and shifted them back to the white bat he was sitting close to. Even though Shadow had always known on the inside that he cared for Rouge more than he let on, it took the event that had recently taken place to finally allow his mind to accept it. And now that it had, Shadow found himself in a position that was unlike anything he had ever faced before and remained unsure as to what to do about it.

The white bat in question began to stretch and soon rose with a yawn. Shadow panicked for a second, he hadn't really thought about her waking so soon, even if he didn't know how long she had been asleep. He also didn't really know why he was down here; he felt he needed a better reason than "just because." Rouge didn't immediately notice him, probably still trying to fully waken, so he decided to go ahead and say something before she did and he looked foolish for just sitting there staring at her.

"Hey, feeling ok?"

Rouge gasped slightly, startled, and quickly turned to face him. She probably hadn't expected someone to be watching her sleeping, least of all him.

"Shadow? I'm fine…Why are you up? You're still hurt!"

Shadow hadn't really thought about his personal condition until Rouge mentioned it, only now noticing the amount of bandages on him, some coated him a light reddish tint.

"I'm fine, just a few scrapes. I've seen worse."

Rouge frowned, obviously not satisfied with his answer.

"If that's a scrape I would hate to see a cut…Well, why don't you let Tails take a look at you? Come on."

Rouge got up from her bed and began to exit the basement, pulling Shadow along with her. The pair walked into the room where Sonic was still watching TV.

"Hey Rouge, see Shadow got you up."

Sonic chuckled after the last few words. Rouge didn't pay him any mind though.

"Funny blue-boy, just cause you don't have Amy around is no reason for you to poke fun."

Sonic cleared his throat and continued watching TV, his fun killed. Amy had finally matured in personality and didn't pester Sonic quite as much, and with her annoying antics finally dying out Sonic was able to see some of her finer qualities. The two had finally become an item of sorts not that long ago, but Amy had gone to visit some family for a couple of weeks in a city on the opposite coast, Felucia. Now that Sonic was subdued some Rouge decided to question him on Tails whereabouts. The fox was always busy with something.

"Have you seen Tails? Since Shadow is up he might as well see how the wounds are."

Shadow frowned.

"Rouge, I told you I'll be fine."

Rouge took another look at Shadow to see how truthful his words spoke. The only real thing that seemed wrong was the bit of crimson on some of his bandages, but that could be enough in the proper environment, Ultimate Lifeform or not.

"Well, at least let Tails take a look. You want to be in top condition the next time we see Eggman don't you?"

Shadow took on a bit more serious expression at the mention of the evil doctor's name, but made no further arguments. Besides, he felt like he had to because she asked him, but didn't know quite why. Sonic came alive at the mention of Eggman's name, remembering now some information he wanted to share.

"Me and Tails went over to where you said that base was at to get a good look at it. The entire place seems to be dead quiet. Eggman's up to something, I can feel it. I wanted to check it out more, but Tails said that it wouldn't be a good idea cause of those damn copies so…"

Tails came into the room just as Tails began to trail off.

"Hey Sonic, is Sha…Oh, good, everyone is here. Take it your feeling better Shadow?"

Shadow only nodded, not really feeling in the mood to talk. Rouge on the other hand had no such feelings.

"He says he is, but can you see? You are the resident medical expert."

Tails perked up.

"Sure, while I take a look at Shadow I have something I would like to tell you all. This way."

The group followed the orange kitsune into his normal lab where he began to unwrap Shadow's bandages as he spoke.

"I figured out a way were we can tell each other apart from our clones. Eggman will probably use the fact that they are practically indistinguishable from us to frame us or start fights amongst ourselves, lowering our trust in each other."

Tails finished the unwrapping and proceeded to look at Shadow's wounds, but found that they had all completely healed up. There was no sign of his previous injuries, something that Tails found utterly amazing, healing that fast was overnight was amazing. He would have to see just how Shadow's healing abilities worked when this was over…

"Seems Shadow has completely healed, all his wounds are gone."

Shadow tossed any remaining bandages into the trash bin and smirked.

"See? Just a scrap."

Rouge thought that Shadow was being too arrogant, but decided to stay quiet so the kitsune would finish with what he had been saying. Tails, who was now finished with attending to Shadow, just sighed and walked over to a computer console and began typing out some commands. The black hedgehog obviously had a bit a Sonic's overconfidence.

"Now, while we won't be able to prove anything the clones do as part of Eggman's agenda, we make it so that the clones can't just replace one of us to keep us from being able to trust one another."

A beep is heard a machine next to the computer Tails was using comes to life. A fine mist begins to emerge from it as the top rises, revealing 5 vials of an unknown, glowing blue substance. Tails picked up one of the vials and held it carefully, showing it to the labs occupants.

"It took me a bit, but I managed to make this serum of nanite's made to be injected directly into the bloodstream. Once in the blood it travels up to the brain and attaches itself to the area that controls your sensory organs, particularly the part that controls your vision. The serum will allow to "feel" anyone else who has the serum also injected into them. And, once fully established and configured to the functions of your individual brain patterns, will allow you to see a faint glow from them as well. It also has a small tracking device in it, so if anything were to happen to us we can be easily located from any device configured to the nanite's particular wavelength."

Shadow didn't really feel comfortable with the whole concept. He really didn't like being injected with anything, previous experiences all unwelcoming. But that wasn't the only reason.

"Wouldn't Eggman be able to detect them? Plus if you can track us then so can he."

Tails took no time in reassuring the group.

"While Eggman may normally be able to detect something like this, it's highly unlikely that he can detect these particular ones. I configured them so that they seem like ordinary proteins; thus they seem more like a natural biological function than nanite's. The frequency of the tracking device is super encrypted, so even if Eggman did notice it he would have a hard time breaking it, I made sure of that. It also has a failsafe to change frequency if that ever happens. Anyway though, Eggman never really looks for this kind of stuff anyway, he is usually only interested in Chaos wavelengths."

Shadow still had his doubts, but decided that he would go along with it anyway, who knows? Might end up being useful. Tails proceeded to administer the nanite serum to himself and the rest of the group. Once this was accomplished Sonic decided to let the group on his "plan of action."

"Alright, here's the deal. After checking out that base with Tails we went over to the Floating Island to update Knuckles on what was going on. We tried to get him to come back with us, but he wouldn't leave his stupid rock with Eggman active again, so we are gonna go over there to get him before we make our way to Eggman's base. He got a recent gash on his hand from some rock-climbing incident, so that's how we can probably tell him apart from any clone that could take his place. That was Tails idea. Anyways, once we hook up with Red we go and kick some ass!"

Rouge sighed; Sonic was always so direct. He was gonna get himself killed one day…Shadow too, but at least he wasn't quite as bad as the blue one.

"Don't you think that's a bit too direct?"

Sonic seemed to think for a moment. To Rouge it was more like blank staring.

"Yeah….well, it's more fun that way."

Sonic let out a big grin, which Rouge wanted to slap off him so bad.

"Fun?" She thought, "being chased by Eggman's war machines and risking my life needlessly is not my idea of fun."

Shadow and Tails seemed to be fine with Sonic's "plan," so she decided not to argue, there would be a time and a place for that.

A few minutes later the group was airborne, taking the Tornado II towards the Floating Island. Tails was piloting while Rouge sat in the co-pilots seat; Sonic and Shadow stood on opposing wings of the aircraft. Most of the way was silent, with the exception of Tails and Rouge occasionally striking up a conversation, but Shadow and Sonic remained silent the entire way. The wind drowned out almost all sound outside of the cockpits, so conversation with the two was not very practical anyway.

A few hours after the start of the trip the group entered the Floating Islands airspace where Tails brought the Tornado to a landing on the southern side of the island. An airstrip had been built there when Eggman had first managed to trick Knuckles into thinking Sonic was his enemy and gained control of the entire island. All the structures that Eggman had constructed here had long been demolished, but Tails had managed to convince Knuckles to leave the airstrip intact for occasions such as this. Once the group had disembarked, Tails hid the plane in its usual hiding place, a growth of thick trees near one end of the airstrip. With the plane hidden, they all began to move towards the center of island, near the mountain's base. This was were the shrine of the Master Emerald was located, and with it, Knuckles. As Shadow followed Sonic in zipping through the dense jungle, something which kept the pair from running at their full speed, Shadow took in some of the sights the island had to offer from ground level. As Tails, who had taken to the air with Rouge as a method of reaching the shrine, had flown over the island Shadow had taken the opportunity to notice several of its features. One thing he found interesting was that on the other side of the approaching mountain there lied a desert, the reason he found this so peculiar was that it was only a small portion directly behind the mountain. The rest of the desert was surrounded by thick jungle.

As Shadow continued to follow Sonic towards the shrine he tired to take note of many of the interesting flora and fauna he had never seen before, some seemingly very unique. Maybe he would come back here when they finished with Eggman. Shadow erupted from his thoughts as Sonic's voice filled his ears, notifying him that they were about the reach their destination. The two blurs burst from the jungle and came to a stop in a small clearing, the Master Emerald shrine being in it's center. Rouge and Tails landed momentarily afterwards, both looking kind of tired with trying to keep up with the two hasty hedgehogs, even if they were not going at top speed. Sonic ran up the stops of the shrine.

"Knuckles! Hey Knux! You here Red?"

A rustle to his left caught Sonic's attention as the echidna came out into the open.

"Sonic! Good to see you could make it, kinda soon though isn't it?"

Sonic motioned towards Shadow.

"Yeah, Shadow here healed up faster than we thought."

Shadow looked towards Sonic at the mention of his name. He had been transfixed on the Master Emerald, he felt as if something was pulling him towards it, calling out to him. Shadow normally only felt this when he had a Chaos Emerald in his possession and was near another emerald. But even then, it was never quite this strong. When Sonic had mentioned his name he decided to ignore the matter and concentrate on the more important matters at hand, the last thing he needed was a bunch of distractions. Knuckles had begun making his way to the top of the shrine in order to join Sonic near the Master Emerald.

"So, what's the plan again blue boy? I want to get this done and over with as soon as possible. Having my island or my emerald threatened isn't something I'm fond of."

Knuckles reached the top of the shrine and stood directly in front of Sonic. The blue hedgehog didn't know why, but he was actually feeling a bit intimidated by the way Knuckles was standing in front of him. Something was wrong. On looking down Sonic found out what it was, the echidna's hand was free from any marks. It was too late for him to make any reaction though; Knuckles had already noticed Sonic's hesitation and knew he was caught. Then, not being one to give up an opportunity, nailed Sonic with all his strength right in the stomach and chest area. Sonic, who hadn't had a chance to put his guard up, doubled over in pain, all the wind knocked out of him. As Sonic felt the impact from Knuckles blow he heard a few ribs crack from its force. A normal person would probably have a huge hole in their chest seeing as how Knuckles was able to destroy large boulders with one hand. Good thing he wasn't normal, but he wasn't invincible either and felt his vision start to blur. Knuckles wasn't done with the blue blur yet though, and decided to take him out while the opportunity was present. After his last blow he whirled around and gave Sonic a hard hit on the back of his neck as he fell towards the floor. It was enough to effective take Sonic out; he had lost consciousness before he even hit the floor.

The remaining three friends hadn't anticipated such a turn of events and couldn't react fast enough, but Shadow was the first to pull into gear. Just as pseudo Knuckles finished his elbow maneuver on Sonic, Shadow gave him a fierce upper cut that sent the offender flying into the air. The black hedgehog then tried his patented homing attack, but Knuckles wasn't stupid and had fought Sonic several times before, so he had grown well versed in dodging and blocking such attacks. Knuckles managed to dodge Shadow and landed on the ground not far from where he had.

"Shadow, wait! That Sonic was a clone, I can prove it!"

Shadow hesitated for a second, not sure whether to trust the echidna whom he had never really met, but then he noticed his hand. He had remembered what Sonic had said they were to use to identify if the echidna was real or not, and this one didn't have any identifying mark.

While Shadow had begun to engage Knuckles, Rouge and Tails ran over to assist Sonic in what ways they could. He was in pretty bad shape, but the kitsune knew it wouldn't be all that much of a problem to get his blue idle back into shape. Sonic had suffered worse than this. Rouge, who saw the look on Tails face, decided to look into Shadow's fight. She knew how Knuckles fought from their previous encounters so she knew several of his weaknesses, but she wondered whether or not she should interfere.

Shadow ran towards Knuckles, who managed to jump over him just in time to avoid the painful blow that was to be dealt him, but not enough to escape Shadow's abilities. As the red echidna flew over him Shadow did a 180, facing him directly, and stretched out his hand.

"_Chaos Spear!_"

Yellow blades of energy shot forth from Shadow's hands, engulfing Knuckles and biting deeply into his flesh. The attack was much more potent than Shadow had been expecting. As Knuckles fell Shadow ran towards him and executed a powerful kick that sent his victim flying towards the Master Emerald Shrine. Pseudo Knuckles had only been minutes into the fight and was already pretty beat up, cuts and bruises covering him. From the looks of it Shadow figured the echidna might be close to finished, but as he finished that though the clone stood up like nothing was wrong, and started laughing. It was only then that Shadow noted that the wounds he had were not bleeding like they normally would.

"What do you think? A gift from the good doctor, nanite's in my blood heal my wounds as they open and keep fatigue from getting to me. You have no chance."

Shadow smirked at the overconfident echidna.

"Fool, nanite's won't heal missing limbs."

Shadow dashed towards the echidna in an attempt to get behind him, but to his surprised the red clone moved fast enough to get out of the attempt. Shadow dashed towards the echidna once more but he again moved out of the way, a new vigor seeming to course through him. The echidna began speaking as he barely managed to dodge some of Shadow's offense.

"Did you know Shadow, that at this moment you and Sonic are destroying Station Square?"

Shadow's ears perked at this, but he concentrated more on causing the red impostor pain than on such information. Or at least he tried to. Knuckles, who Shadow noted was a bit faster, grinned evilly as he dodged the black and red hedgehogs next move.

"Do you know how many the both of you have probably killed by now? More than 12,000 I would say…"

Shadow knew something like that would probably have happened at one point or another, but the information given to him so plainly fed his already bursting anger.

"_YOU BASTARD!"_

Shadow felt his rage build up, then burst forth, giving him great amounts of energy for only but a moment.

"_Chaos Control!_"

Shadow appeared directly behind Knuckles and planted his hand directly into the red echidna's back.

"_Chaos Spear!_"

White-hot bolts of energy tore through Knuckles chest, blood gushing forth from the many wounds. Shadow turned and kicked Knuckles into the ground with enough force to make an outline of his body in the ground, then he landed next to Knuckles and picked him up by the neck and glared at him dangerously.

"Now…your going to tell me where Eggman is and what his plans are, and I had better be satisfied with your answers"

Knuckles seemed to struggle with his words for a minute before finally speaking.

"I…have only…one thing…to say to you…good bye."

Knuckles gave Shadow a blow that was hard enough for him to loosen the grip he had on the fake echidna so he could get free. Shadow immediately tried to re-secure his hold on the clone, but when the echidna hit the ground a while engulfed him, leaving no trace of his former presence. Shadow growled.

"Damn."

Rouge came over to Shadow now that he was done with the fight.

"He probably had one of Eggman's teleportation devices…Shadow, we should go, Sonic has a few cracked ribs caused by Knuckles punch and does need a bit of medical attention. Plus we still need to figure out what to do next and what happened to the original Knuckles."

Shadow nodded and walked with Rouge to where Tails had been doing what he was able to for Sonic.

"Shadow, can you and Rouge help me carry Sonic? Knuckles, the original one anyway, has a place at the mountains base that has most of the supplies I need to fix Sonic up with."

The group had to be careful when they picked up the blue hedgehog, not wanting to cause him any more injuries than he currently had. The area Tails brought them to wasn't very far from the shrine. It was a cave carved into the side of Death Mountains base, and from its looks it was fairly obvious that it was man-made so to speak. The deep scratches in some walls and the unnatural smoothness on others was evidence enough. Also in addition to that was the lack of anything you would normally find in naturally formed caverns, like stalagmites and such. The entrance to cavern was more or less the size of regular door that opened up to a fair sized chamber branching of in different directions, each leading to different rooms. Tails had the pair place Sonic in one of the adjacent rooms while we went to find what medical supplies he could. On his return he began to treat Sonic for what he could.

"We are going to have to stay here for a while. I'm sure it goes without saying but I heard everything that clone said. And, knowing the military, the first place they will probably look for us is at my workshop. Later on I am going to have to return there though, there is some equipment there I will need as well as the Chaos Emerald Shadow brought back with him."

Shadow had almost forgotten about the emerald, and now that he did remember he wished he had it with him. It would have given him a nice boost for what he was about to go do…he might have to go for it anyway, he really did need that boost.

"You and Rouge stay here then, I'm going to pay myself a visit."

Rouge already knew what Shadow was thinking of.

"Shadow! No! Remember what happened last time? What makes you think you can just take them out now?"

Shadow had already started to leave, his mind set.

"Last time we were in a Chaos proof room, this time I wont be. Not to mention I'll have a Chaos Emerald as well, that gives me an advantage. Tails, where is the emerald anyway? I'm usually able to sense Chaos energy and I never sensed the one at your workshop."

Tails grinned before answering.

"Yeah…Eggman has always been very persistent with trying to find the emeralds, so I made a type of jammer that blocks off Chaos wavelengths. Its made almost in the same manner that Chaos resistant metals are, but its not nearly as hard or expensive. It's light too, I have one on the Tornado II as well."

Shadow sighed.

"That's great Tails, but not quiet what I was asking."

Tails blushed slightly, realizing he got carried away.

"Sorry…the basement under the shop is divided into two parts, the room beyond the metal door has a safe hidden underground. You will have to look for the button to raise it, its hidden on the wall right of where you will enter. Here is the passkey for the door. The safe has two emeralds by the way, yours and one me and Sonic had found some time ago."

Shadow pocketed the key Tails gave him. Two emeralds…he liked that, they would boost his power a fair amount…but three…

"Tails, your plane can fly without the use of its Chaos Emerald right?"

Tails eyed Shadow a moment, he knew what the black hedgehog was thinking and didn't particularly like it. Shadow wanted to take the Tornado's emerald, but know was no time to be selfish or untrusting, so he decided to go along with him.

"Yeah…it has fuel cells that are charged with power in case anything ever happens to the emerald. You can take it, but don't lose it."

Shadow nodded.

"Great, thanks."

As he started to leave Rouge blocked his way by putting a hand on his chest.

"Hey...don't go and do something stupid, ok?"

Rouge let Shadow go and gave him a quick peck on the lips before walking off. Shadow found himself very much surprised and at a loss for words, so merely nodding he continued on his way. He tried not to let himself thinking about it anymore than necessary, so trying his best he pushed the event into the back of his mind and blasted off full speed towards the Tornado. Now that he knew the way he was able to cover the ground in seconds, reaching the plane much faster than when they had left it. Shadow walked over to where the Chaos emerald had been stored, only to find it missing.

"Shit!" Shadow exclaimed and hit the side of the plane, denting it slightly. Three emeralds would have given him a good advantage, but now he could only hope that the other two emeralds in Tails workshop had not also been taken. Shadow quickly performed Chaos Control and appeared at Tails' workshop in a flash of light. On entering Shadow found that everything was still as they had left it. If what Tails' said was true, then the military must still be engaged with his and Sonic's clones in Station Square. He entered the basement and used the key to gain entry to the walled off area. It was really messy, part from all kinds of different machines in the process of being constructed lay scattered about. There were two long tables on either side of the rooms walls. One of which sported a really high-tech looking computer, the other parts to some kind of machine Tails' was building and various schematics to accompany it. Shadow began searching along the wall for the button, eventually finding it hidden in a portion of false wall. As he hit the switch the hum of machinery could be heard as the center portion of the floor began to rise, reveling a large, black meta safe. Approaching the safe, Shadow found a card slot and inserted the key card Tails had given him. The safe granted him access, the hiss of the locks unengaging heard before the door opened. As it did Shadow could feel the combined power of the two emeralds lash out, calling to him. This feeling was rushed by his anticipation as he reached in to pull the emeralds out. As Shadow held the emeralds in his hand he could feel his power multiply. This, however, was not normal. As his mind got more used to this new vigor coursing through him, he was able to see just how abnormal this was. His body had become engulfed in green flames of Chaos energy, while the emeralds themselves where disintegrating and being absorbed by his body. Normally, this only happened when one used all seven gems to achieve a higher level of power. Whenever he held a Chaos Emerald before he had only been able to use a portion of its energy to call forth different Chaos attacks or amplify his natural ones. The more emeralds he had the more he could use the attacks and the more powerful they would become. But now with the Emeralds being absorbed into them, he could use all of their power. The Chaos fueled flames had died down by now as Shadow had completely finished taking in the essence of both Emerealds. For a moment Shadow wondered what he would do if he ever needed the emeralds back in their physical form, but decided not to worry about it just yet. Instead, he tried to sense the limits of his new power, finding it in likeliness to being in his super form, but watered down a bit. He noted that his muscles had tightened and gained a better tone to them, making him physically stronger than he was before. Shadow also noticed that his senses seemed sharpened, and they already been pretty sharp to begin with. He smiled at this new outcome, though part of him wondered why it never happened before, but he decided not to complain. Forming a picture of Station Square in his mind, he called on the power of Chaos Control once more and disappeared in a flash of light, leaving behind only a scorch mark to prove he had been there.


End file.
